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add config
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Leila011 committed Jul 31, 2024
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63 changes: 63 additions & 0 deletions src/agat/agat_sp_add_introns/config.vsh.yaml
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name: agat_sp_add_introns
namespace: agat
description: |
The script aims to add intron features to gtf/gff file without intron features.
keywords: [gene annotations, GTF conversion]
links:
homepage: https://github.com/NBISweden/AGAT
documentation: https://agat.readthedocs.io/en/latest/tools/agat_sp_add_introns.html
issue_tracker: https://github.com/NBISweden/AGAT/issues
repository: https://github.com/NBISweden/AGAT
references:
doi: 10.5281/zenodo.3552717
license: GPL-3.0
authors:
- __merge__: /src/_authors/leila_paquay.yaml
roles: [ author, maintainer ]

argument_groups:
- name: Inputs
arguments:
- name: --gff
alternatives: [-f, --ref, -reffile]
description: Input GTF/GFF file.
type: file
required: true
direction: input
example: input.gff
- name: Outputs
arguments:
- name: --output
alternatives: [-o, --out, --outfile, --gtf]
description: Output GFF3 file.
type: file
direction: output
required: true
example: output.gff
- name: Arguments
arguments:
- name: --config
alternatives: [-c]
description: |
String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the original agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently).
type: file
required: false
example: custom_agat_config.yaml
resources:
- type: bash_script
path: script.sh
test_resources:
- type: bash_script
path: test.sh
- type: file
path: test_data
engines:
- type: docker
image: quay.io/biocontainers/agat:1.4.0--pl5321hdfd78af_0
setup:
- type: docker
run: |
agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.txt
runners:
- type: executable
- type: nextflow

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